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The diversity of lichen photobionts is not fully known. We studied here the diversity of the photobionts associated withCladonia, a sub-cosmopolitan genus ecologically important, whose photobionts belong to the green algae genusAsterochloris. The genetic diversity ofAsterochloriswas screened by using the ITS rDNA and actin type I regions in 223 specimens and 135 species ofCladoniacollected all over the world. These data, added to those available in GenBank, were compiled in a dataset of altogether 545Asterochlorissequences occurring in 172 species ofCladonia. A high diversity ofAsterochlorisassociated withCladoniawas found. The commonest photobiont lineages associated with this genus areA. glomerata,A. italiana, andA. mediterranea. Analyses of partitioned variation were carried out in order to elucidate the relative influence on the photobiont genetic variation of the following factors: mycobiont identity, geographic distribution, climate, and mycobiont phylogeny. The mycobiont identity and climate were found to be the main drivers for the genetic variation ofAsterochloris. The geographical distribution of the differentAsterochlorislineages was described. Some lineages showed a clear dominance in one or several climatic regions. In addition, the specificity and the selectivity were studied for 18 species ofCladonia. Potentially specialist and generalist species ofCladoniawere identified. A correlation was found between the sexual reproduction frequency of the host and the frequency of certainAsterochlorisOTUs. SomeAsterochlorislineages co-occur with higher frequency than randomly expected in theCladoniaspecies.

Numerous species of microscopic fungi inhabit mosses and hepatics. They are severely overlooked and their identity and nutritional strategies are mostly unknown. Most of these bryosymbiotic fungi belong to the Ascomycota. Their fruit-bodies are extremely small, often reduced and simply structured, which is why they cannot be reliably identified and classified by their morphological and anatomical characters. A phylogenetic hypothesis of bryosymbiotic ascomycetes is presented. New sequences of 78 samples, including 61 bryosymbionts, were produced, the total amount of terminals being 206. Of these, 202 are Ascomycetes. Sequences from the following five gene loci were used: rDNA SSU, rDNA LSU, RPB2, mitochondrial rDNA SSU, and rDNA 5.8S. The program TNT was used for tree search and support value estimation. We show that bryosymbiotic fungi occur in numerous lineages, one of which represents a newly discovered lineage among the Ascomycota and exhibits a tripartite association with cyanobacteria and sphagna. A new genus Trizodia is proposed for this basal clade. Our results demonstrate that even highly specialized life strategies can be adopted multiple times during evolution, and that in many cases bryosymbionts appear to have evolved from saprobic ancestors. © The Willi Hennig Society 2009.

This study was focused on two species of lichen-forming fungi from Madagascan Region whose taxonomy has been controversial over the years, Cladonia mascarena Nyl. and Heterodea madagascarea Nyl. While some authors considered C. mascarena to belong to Cladonia, others place it in Pycnothelia Dufour. In this study three loci (ITS rDNA, rpb2 and ef1 alpha) were used to determine the phylogenetic placement of C. mascarena. Our results show that it belongs to Pycnothelia and the combination Py cnothelia mascarena (Nyl.) Nyl. is substantiated. In addition, a key to the genus Pycnothelia is provided. The morphological study of new specimens of Gymnoderma coccocarpurn Nyl. and H. madagascarea concluded that these taxa belong to a same species, confirming the extension of Gymnoderma Nyl. to Africa. The overlooked genus Baeoderma Vain. is regarded as a synonym of Gymnoderma, and its type species Baeoderma madagascareum (Nyl.) Vain. is referred to G. coccocarpum.

The lichen speciesCladonia angustilobais characterized by a well-developed primary thallus and narrow squamules which show deep incisions, and the presence of usnic and fumarprotocetraric acids. Morphologically it is similar toC. foliaceaandC. convoluta, from which it can be distiguished by the squamule size and morphology. Since similar characters were used to distinguishC. foliaceafromC. convolutawhich do not represent different lineages, it is necessary to examine the taxonomic status ofC. angustilobaby means of DNA sequences. In this study, the species delimitation within theC. foliaceacomplex was studied by sequencing three loci, ITS rDNA,cox1andRPB2. The data were analyzed by means of phylogenetic and species delimitation methods (GMYC, PTP, ABGD and BPP). Our results show that none of the three species is monophyletic. Most of the species delimitation methods did not support the current species as evolutionary lineages. Only some of the BPP analyses supportedC. angustilobaas a species distinct fromC. foliaceaandC. convoluta. However, the hypothesis that considers theC. foliaceacomplex as constituted by a unique species obtained the best Bayes Factor value. Therefore,C. angustilobaandC. convolutaare synonymized withC. foliacea.A new, thoroughly checked synonymy with typifications of the wholeC. foliaceacomplex is presented. An updated survey of the world distribution data is compiled.

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN. Publisher’s Note A first version of this text was prepared by the first eight authors and the last one, given here. The other listed co-authors in the article PDF support the content, and their actual contributions varied from only support to additions that substantially improved the content. The full details of all co-authors, with their affiliations, are included in Supplementary Table 1 after p.175 of the article for reasons of clarity and space. Slavomír Adamčík Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23 Bratislava, Slovakia Teuvo Ahti Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland M. Catherine Aime Purdue University, 915 W. State St., West Lafayette, Indiana 47907, U.S.A. A. Martyn Ainsworth Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom László Albert Hungarian Mycological Society, 1087 Könyves Kálmán krt. 40, Budapest, Hungary Edgardo Albertó Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, Universidad Nacional de San Martin-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina Alberto Altés García Facultad de Biología, Ciencias Ambientales y Química, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain Dmitry Ageev SIGNATEC Ltd., 630090, Novosibirsk, Akademgorodok (Novosibirsk Scientific Center), Inzhenernaya str., 22, Russia Reinhard Agerer Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 München, Germany Begona Aguirre-Hudson Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom Joe Ammirati University of Washington, Seattle, Washington 98195-1800, U.S.A. Harry Andersson Eichhahnweg 29a, 38108 Braunschweig, Germany Claudio Angelini Jardín Botánico Nacional Dr. Rafael Ma. Moscoso, Apartado 21-9, Santo Domingo, Dominican Republic Vladimír Antonín Moravian Museum, Zeny trh 6, 659 37 Brno, Czech Republic Takayuki Aoki Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan André Aptroot ABL Herbarium, G.v.d.Veenstraat 107, 3762 XK Soest, The Netherlands Didier Argaud 40 rue du Justemont, 57290 Fameck, France Blanca Imelda Arguello Sosa Instituto Tecnológico de Ciudad Victoria, Tecnológico Nacional de México, Ciudad Victoria, Tamaulipas, Mexico Arne Aronsen Torødveien 54, 3135 Torød, Norway Ulf Arup Biological Museum, Lund University, Box 117, 221 00 Lund, Sweden Bita Asgari Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization, Tehran, Iran Boris Assyov Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Str., 1113 Sofia, Bulgaria Violeta Atienza Facultad de Ciencias Biológicas, Universitat de València, C/Dr Moliner 50, 46100, Burjasot, Valencia, Spain Ditte Bandini Panoramastr 47, 69257 Wiesenbach, Germany João Luís Baptista-Ferreira Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal Hans-Otto Baral Blaihofstr. 42, 72074 Tübingen, Germany Tim Baroni The State University of New York, 340 Bowers Hall, P.O. 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Boomsluiter T.v.Lohuizenstraat 34, 8172xl, Vaassen, The Netherlands Jan Borovička Institute of Geology, Czech Academy of Sciences, Rozvojova 269, 165 00 Prague 6, Czech Republic Tor Erik Brandrud Norwegian Institute for Nature Research, Gaustadalleen 21, 0349 Oslo, Norway Uwe Braun Martin-Luther-Universität, Institut für Biologie, Bereich Geobotanik, und Botanischer Garten, Herbarium, Neuwerk 21, 06099 Halle, Germany Irwin Brodo Canadian Museum of Nature, 240 McLeod Street, Ottawa, Ontario, Canada Tatiana Bulyonkova A.P. Ershov Institute of Informatics Systems, Russian Academy of Sciences, Siberian Branch, 6 Acad. Lavrentjev pr., Novosibirsk 630090, Russia Harold H. Burdsall Jr. Fungal & Decay Diagnostics, LLC, 9350 Union Valley Road, Black Earth, Wisconsin 53515, U.S.A. Bart Buyck Muséum National d’Histoire Naturelle, CP 39, ISYEB, UMR 7205 CNRS MNHN UPMC EPHE, 12 rue Buffon, 75005 Paris, France Ana Rosa Burgaz Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain Vicent Calatayud Fundación CEAM, c/ Charles R. Darwin, 14, Parque Tecnológico, 46980 Paterna, Valencia, Spain Philippe Callac INRA, MycSA, CS 20032, 33882 Villenave d’Ornon, France Emanuele Campo Associazione Micologica Bresadola, Via Alessandro Volta 46, 38123 Trento, Italy Massimo Candusso Via Ottone Primo 90, 17021, Alassio, Savona, Italy Brigitte Capoen Queffioec, rue de Saint Gonval, 22710 Penvenan, France Joaquim Carbó Roser, 60, 17257 Torroella de Montgrí, Girona, Spain Matteo Carbone Via Don Luigi Sturzo 173 16148 Genova, Italy Rafael F. Castañeda-Ruiz Instituto de Investigaciones Fundamentales en Agricultura, Tropical ‘Alejandro de Humboldt’, OSDE, Grupo Agrícola, Calle 1 Esq. 2, Santiago de Las Vegas, C. Habana 17200, Cuba Michael A. 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Zhurbenko Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia The following institutions are also supporting the present text (institutional support means that committees from the mentioned) Asociación Micológica Carlos Spegazzini (Argentina) Austrian Mycological Society (Austria) Croatian Mycological Society (Croatia) Committee of the Czech Scientific Society for Mycology (Czech Republic) The Netherlands Mycological Society (The Netherlands) Sociedad Española de Liquenología (Portugal/Spain) Iberian Mycological Society (which is under constitution, Portugal/Spain) Federación de Asociaciones Micológicas Andaluzas (FAMA) (Spain) Asociación Botánica y Micológica de Jaén (Spain) Asociación Micológica Hispalense Muscaria (Spain) Societat Micològica Valenciana (Spain)

Pino-Bodas, R., Ahti, T. & Stenroos, S. 2017. Cladoniaceae of the Azores. — Herzogia 30: 445 — 462. Based on material collected from 40 localities on four islands of the Azores, three species of Cladonia are new to Macaronesia: C. conista, C. mauritiana and C. novochlorophaea and four are new to the Azores: C. bellidiflora, C. dimorpha, C. rei and Cladonia sp. In addition, several species are new to individual islands of the archipelago. Cladonia dactylota is new to continental Europe (SW France). Cladonia stereoclada, described from the Azores, is lectotypified. These data are complemented with annotations on species distribution and chemical variations. Uncertain specimens were sequenced to confirm the species identities.

Correction DOI:10.3897/mycokeys.19.11562 We explored whether DNA-phylogeny-based and morphology-based genus concepts can be reconciled in the basidiomycete family Phanerochaetaceae. Our results show that macromorphology of fruiting bodies and hymenophore construction do not reflect monophyletic groups. However, by integrating micromorphology and re-defining genera, harmonization of DNA phylogeny and morphological genus concepts is possible in most cases. In the case of one genus (Phlebiopsis), our genetic markers could not resolve genus limits satisfactorily and a clear morphological definition could not be identified. We combine extended species sampling, microscopic studies of fruiting bodies and phylogenetic analyses of ITS, nLSU and rpb1 to revise genus concepts. Three new polypore genera are ascribed to the Phanerochaetaceae: Oxychaete gen. nov. (type Oxyporus cervinogilvus), Phanerina gen. nov. (type Ceriporia mellea), and Riopa (including Ceriporia metamorphosa and Riopa pudens sp. nov.). Phlebiopsis is extended to include Dentocorticium pilatii, further species of Hjortstamia and the monotypic polypore genus Castanoporus. The polypore Ceriporia inflata is combined into Phanerochaete. The identity of the type species of the genus Riopa, R. davidii, has been misinterpreted in the current literature. The species has been included in Ceriporia as a species of its own or placed in synonymy with Ceriporia camaresiana. The effort to properly define R. davidii forced us to study Ceriporia more widely. In the process we identified five closely related Ceriporia species that belong to the true Ceriporia clade (Irpicaceae). We describe those species here, and introduce the Ceriporia pierii group. We also select a lectotype and an epitype for Riopa metamorphosa and neotypes for Sporotrichum aurantiacum and S. aurantium, the type species of the anamorphic genus Sporotrichum, and recommend that teleomorphic Riopa is conserved against it.

In our ongoing study of the genus Cladonia, we have encountered several specimens that have proved to represent undescribed species. Four of them are described here as new. Cladonia camerunensis (Cameroon) resembles C. didyma (Fée) Vain., but the former has a coarsely granular surface and a melanotic podetial base; C. compressa (Bolivia) is distinguished by a dominant primary thallus and deeply divided and phyllopodiate podetia; C. longisquama (Seychelles) has well-developed squamules and contains barbatic acid; C. vescula (Bolivia, Peru) differs from C. peziziformis (With.) J. Laundon by an ecorticate podetial surface and the production of homosekikaic acid. The names C. aspera Ahti & Kashiw. and C. crinita (Delise ex Pers.) Ahti are shown to be illegitimate later homonyms and are replaced by the names C. asperula and C. perfoliata, respectively. The neglected name C. botryoides (Tuck.) Vain. is shown to be a synonym of C. squamosa. Another overlooked name, C. crinita Bertol., is shown to be the earliest name for C. evansii, but we propose to retain the latter through conservation. The typification of C. beaumontii Tuck. is amended. Cladonia conspicua is reinstated on the basis of new data. New range extensions in Canada and the United States are given for the poorly documented species C. oricola.

Cladoniais one of the largest lichen-forming ascomycete genera. It was formerly divided into ten sections, three of which,Crustaceae(Cladina),Tenues, andImpexae, are called the reindeer lichens. While previous studies have elucidated the relationships between species and sections, they often examined only one or a few specimens of each species in the analysis. This study examined the monophyly of selected members of sectionsCrustaceae,Tenues, andImpexaeand their relationships in the genusCladoniausing the internal transcribed spacer region of the nuclear ribosomal DNA (ITS rDNA) and the mitochondrial small subunit gene of the mitochondrial ribosomal DNA (mtSSU). The phylogenetic tree contained four clades, two representing species in sectionImpexae, one representing species that belong to sectionsCrustaceaeandTenues, and one clade withC. arbusculaand related species. Five of 22 species,C. pycnoclada,C. stellaris,C. evansii,C. ciliataandC. subtenuis, showed monophyly in the phylogenetic tree; some of these 5 species have been shown previously to be monophyletic. The thallus branching pattern was interpreted as an important heritable character using the mtSSU network. Three duplets of paraphyletic species were further examined using ITS rDNA haplotype networks and AMOVA analysis. The results for the species duplets showed some mixing of haplotypes but the AMOVA analysis provided support for species separation within the duplets. While the evidence supports distinct species, further study is needed to conclusively show separate species in these duplets.

Cladoniaceae is a family of lichenized fungi that belongs to the Lecanorales, Ascomycota. The family is distributed widely, although several genera are restricted to the Southern Hemisphere. The circumscriptions of the genera and species in the family have traditionally been based on thallus morphology, the type of vegetative propagules and the secondary metabolites. However, numerous species are highly variable phenotypically, making their delimitation problematic. In the present study a new phylogeny of Cladoniaceae is constructed using five loci (ITS rDNA, IGS rDNA, RPB2, RPB1, EF-1a) from a worldwide sample of 643 specimens representing 304 species. Cladoniaceae was resolved as a monophyletic group. The circumscription of the genera and the relationships among them are discussed. Pycnothelia, Carassea and Metus are closely related, forming a sister clade to the larger genus Cladonia. Cladia in its recent wide sense turned out to be paraphyletic, including species that have been recognized in Thysanothecium and Notocladonia. Cladonia was resolved as monophyletic, with C. wainioi as the earliest diverging lineage. Eleven major clades were resolved in Cladonia. No synapomorphies were found for most of them. We propose the new genera Pulchrocladia and Rexia, as segregates of Cladia, five new combinations, and the resurrection of the genus Heterodea., This study received funding from the Academy of Finland Grant No. 211171 and the SYNTHESYS ES-TAF-922 (S. Stenroos); the European Union’s Seventh Framework Program under Grant No. PIEFGA-2013-625653; Juan de la CiervaIncorporacion no. 2015-23526; Spanish Ministry of Economy, Industry and Competitiveness (MINECO) (R. Pino-Bodas); and the project CGL2013-41839-P led by A. R. Burgaz (T. Ahti and R. Pino-Bodas).

The species from Cladonia section Unciales are characterized by the absence of squamules and soredia on the corticate podetia and the presence of usnic acid. Different subspecies, varieties and forms have been distinguished in the type species C. uncialis. In this study, a molecular phylogeny of Cladonia uncialis and members of the traditionally recognized section Unciales, along with additional potentially allied species, was constructed. DNA sequences from three gene loci, namely ITS rDNA, IGS rDNA and ß-tubulin, were analyzed using Maximum Parsimony, Maximum Likelihood, and Bayesian methods. Eleven species were analyzed for the first time using DNA sequence data. Cladonia uncialis subsp. uncialis and subsp. biuncialis were recognized as distinct taxa. The recognition of C. pseudostellata as a species was not supported by the analyses, but it represents a hypothamnolic acid chemotype, which is reported here as new to Europe (Scotland). The presence of subsp. biuncialis in North America (Newfoundland) was substantiated. The subsp. uncialis usually lacks squamatic acid, but in the eastern United States a morph referred to as subsp. uncialis does normally contain that acid. However, this morph did not attain taxonomic recognition based on phylogenetic analyses. All the other taxa formerly included in sect. Unciales turned out to belong to other groups of Cladonia, mainly Amaurocraeae, Borya, Divaricatae, and Perviae. The formerly recognized genus Cladina (reindeer lichens) is non-monophyletic, consisting of three groups within Cladonia, making the concept Cladina even nomenclaturally useless. Alternative topology tests rejected the monophyly of C. pseudostellata, section Unciales and Cladina.

e lichen Cladonia corymbescens (Cladoniaceae, Ascomycota) has been reported to have two main ranges, one in Melanesia and Australasia and another in the Himalayas and surrounding areas. When specimens from New Caledonia, Bhutan, and �怀ailand were subjected to molecular sequencing (ITS rDNA and RPB2), two distinct clades were detected. �怀e clades were also supported by morphological and geographical di�耀erences supporting recognition of two distinct species. Cladonia corymbescens s. str. is present in the Philippines, Melanesia, and Australasia, while the South East Asian mainland material is referred to C. pseudo�耀ssa, a new combination at species level.

Though most of the lichenicolous fungi belong to the Ascomycetes, their phylogenetic placement based on molecular data is lacking for numerous species. In this study the phylogenetic placement of 19 species of lichenicolous fungi was determined using four loci (LSU rDNA, SSU rDNA, ITS rDNA and mtSSU). The phylogenetic analyses revealed that the studied lichenicolous fungi are widespread across the phylogeny of Lecanoromycetes. One species is placed in Acarosporales, Sarcogyne sphaerospora; five species in Dactylosporaceae, Dactylospora ahtii, D. deminuta, D. glaucoides, D. parasitica and Dactylospora sp.; four species belong to Lecanorales, Lichenosticta alcicorniaria, Epicladonia simplex, E. stenospora and Scutula epiblastematica. The genus Epicladonia is polyphyletic and the type E. sandstedei belongs to Leotiomycetes. Phaeopyxis punctum and Bachmanniomyces uncialicola form a well supported clade in the Ostropomycetidae. Epigloea soleiformis is related to Arthrorhaphis and Anzina. Four species are placed in Ostropales, Corticifraga peltigerae, Cryptodiscus epicladonia, C. galaninae and C. cladoniicola comb. nov. (= Lettauia cladoniicola). Three new species are described, Dactylospora ahtii, Cryptodiscus epicladonia and C. galaninae., This study has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no. PIEF-GA-2013-625653 ‘CLADOF’. R. Pino-Bodas thanks the MINECO for a Juan de la Cierva-Incorporación no. 2015-23526 support. Study of M.P. Zhurbenko was carried out within the framework of the research project of the Komarov Botanical Institute Russian Academy of Sciences (St. Petersburg, Russia) no. 01201255602 and financially supported by the grant of the Russian Foundation for Basic Research no. 14-04-01031 ‘Lichenicolous fungi of Northwest Caucasus

The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 635 newly generated and 3307 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, Candelariomycetidae). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module (Hypha) of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach. Fil: Passo, Alfredo. Universidad Nacional del Comahue. Centro Regional Universitario Bariloche; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Patagonia Norte. Instituto de Investigación en Biodiversidad y Medioambiente; Argentina

Phylogenetic relationships of Stereocaulon with emphasis on the crustose taxa were studied based on nuclear ribosomal ITS1–5.8S–ITS2 and partial beta-tubulin sequences. The placement of four of the six crustose species currently included in the genus has previously been confirmed based on molecular data. It has, however, remained unresolved whether the crustose growth form is a plesiomorphic or apomorphic feature within Stereocaulon, due to contradictory placements of the crustose species in earlier studies. The aim of this study was to clarify the position of the crustose species by including additional data, especially of S. nivale and S. plicatile, which have not been included in previous analyses. The inclusion of S. plicatile in the genus is of particular interest as it is the only species in the genus with submurifrom to muriform ascospores. Altogether 37 specimens representing 31 species of the ingroup, including all the crustose Stereocaulon species, were incorporated in the analyses. Conventional, as well as direct optimization parsimony, maximum likelihood and Bayesian analyses were performed. The results show that the crustose species do not form a monophyletic entity and that the crustose growth form is a plesiomorphic feature within Stereocaulon. The crustose S. nivale and S. plicatile are nested within the genus and their inclusion in Stereocaulon is thereby confirmed. The nested position of S. plicatile indicates that the submuriform to muriform spore type has been gained independently within the genus. Here, S. plicatile is also reported for the first time from Scandinavia.

A new generic name, Rexiella, is published to replace the recently published name Rexia S. Stenroos, Pino‐Bodas and Ahti, which turned out to be an illegitimate later homonym of the cyanobacterial genus Rexia D. A. Casamatta, S. R. Gomez and J. R. Johansen.

Zeorin-containing red-fruitedCladoniaspecies, the so-calledC. cocciferagroup, are widespread terrestrial lichens which share most of their secondary substances but differ morphologically. The main objective of this study was to explore whether the current delimitation of these species is supported by molecular data. A total of 52 European and North American specimens ofC. coccifera,C. deformis,C. diversa, andC. pleurotawere examined. The internal transcribed spacer regions of the nuclear ribosomal DNA and the β-tubulin gene loci were sequenced for phylogenetic analyses. Traditional morphological species circumscriptions in zeorin-containing members of theC. cocciferagroup are not supported by molecular data.Cladonia coccifera,C. deformis, andC. pleurotawere recovered as polyphyletic in both gene topologies;C. diversaformed a lineage in the ITS phylogeny but this was not statistically supported. We detected chemical patterns of the presence/absence of porphyrilic and/or isousnic acid which may help to characterize two lineages. Our results also show incongruence between the two molecular markers studied. Therefore, we focused on possible explanations of this phenomenon. Five major evolutionary mechanisms can potentially result in phylogenetic discordance between genes: presence of pseudogenes, horizontal gene transfer, gene paralogy, incomplete lineage sorting, and hybridization. These mechanisms are briefly discussed. We consider incomplete lineage sorting and/or hybridization to best explain the incongruence.

The complex Cladonia mediterranea belongs to the section Impexae and is formed by C. azorica, C. macaronesica and C. mediterranea. These species are basically distributed in the Mediterranean and Macaronesian Regions. In the present work the limits between the species of this complex are re-examined. To this end, the morphological characters were studied along with the secondary metabolites and the DNA sequences from three loci (ITS rDNA, IGS rDNA and rpb2). The morphological data were studied by principal component analysis (PCA), while the DNA sequences were analyzed using several approaches available to delimit species: genealogical concordance phylogenetic species recognition, species tree (BEAST* and spedeSTEM) and cohesion species recognition. In addition, the genealogical sorting index was used in order to assess the monophyly of the species. The different procedures used in our study turned out to be highly congruent with respect to the limits they establish, but these limits are not the ones separating the prior species. Either the morphological analysis or the different approaches to species delimitation indicate that C. mediterranea is a different species from C. macaronesica, while C. azorica and C. macaronesica, which are reduced to synonyms of C. portentosa, constitute a separate lineage.

We present ataxonomic revision of the ‘manna lichens’ based on morphological, chemical, ecological and molecular data. A large number of herbarium specimens and fresh collections were examined. Phylogenetic analyses were performed using nuclear ribosomal (nrITS, nrLSU) and mitochondrial small subunit (mtSSU) sequences. Some notable phenotypic characters were plotted on the phylogenetic tree, and the analysis reveals that some of these characters are useful for genus and species level distinction of certain ‘manna lichens.’ Phylogeny of the Megasporaceae was revised using a combined data set of nrLSU and mtSSU and performing parsimony and Bayesian analyses. Five genera (Aspicilia, Circinaria, Lobothallia, Megaspora and Sagedia) are recognized. Further, the relationships of five presumably closely related genera of ‘manna lichens’, namely Agrestia (vagrant), Aspicilia (crustose) Circinaria (crustose), Chlorangium (vagrant) and Sphaerothallia (vagrant) with different growth forms were analysed. The analyses revealed that ‘manna lichens’ do not form a monophyletic group but occur in different clades within the genus Circinaria. The genera Agrestia, Chlorangium and Sphaerothallia are assigned as new synonyms under the genus Circinaria and no vagrant or erratic species remain in the genus Aspicilia. The analyses also show that five new erratic, vagrant and crustose species can be recognized. In this study two ‘manna lichens’, viz. Circinaria rostamii sp. nov. (Azerbaijan, Iran and Turkey), and Circinaria gyrosa sp. nov. (Armenia, Azerbaijan, Iran, Turkey, Turkmenistan and Spain) are described as new to science. Three potentially new species with crustose and erratic forms need additional study. Aspicilia fruticolosofoliacea is reduced to synonymy under C. alpicola, and a lectotype is designated for C. aspera. Thirteen new combinations in Circinaria are presented. The phenomenon of vagrancy is briefly discussed, and the biogeography of the ‘manna lichens’ is outlined. Illustrations, distribution maps, and an identification key to the species are provided.

The resolution of the phylogenetic relationships within the order Teloschistales (Ascomycota, lichen-forming-fungi), with nearly 2000 known species and outstanding phenotypic diversity, has been hindered by the limitation in the resolving power that single-locus or two-locus phylogenetic studies have provided to date. In this context, an extensive taxon sampling within the Teloschistales with more loci (especially nuclear protein-coding genes) was needed to confront the current taxonomic delimitations and to understand evolutionary trends within this order. Comprehensive maximum likelihood and Bayesian analyses were performed based on seven loci using a cumulative supermatrix approach, including protein-coding genes RPB1 and RPB2 in addition to nuclear and mitochondrial ribosomal RNA-coding genes. We included 167 taxa representing 12 of the 15 genera recognized within the currently accepted Teloschistineae, 22 of the 43 genera within the Physciineae, 49 genera of the closely related orders Lecanorales, Lecideales, and Peltigerales, and the dubiously placed family Brigantiaeaceae and genus Sipmaniella. Although the progressive addition of taxa (cumulative supermatrix approach) with increasing amounts of missing data did not dramatically affect the loss of support and resolution, the monophyly of the Teloschistales in the current sense was inconsistent, depending on the loci-taxa combination analyzed. Therefore, we propose a new, but provisional, classification for the re-circumscribed orders Caliciales and Teloschistales (previously referred to as Physciineae and Teloschistineae, respectively). We report here that the family Brigantiaeaceae, previously regarded as incertae sedis within the subclass Lecanoromycetidae, and Sipmaniella, are members of the Teloschistales in a strict sense. Within this order, one lineage led to the diversification of the mostly epiphytic crustose Brigantiaeaceae and Letrouitiaceae, with a circumpacific center of diversity and found mostly in the tropics. The other main lineage led to another epiphytic crustose family, mostly tropical, and with an Australasian center of diversity the Megalosporaceae - which is sister to the mainly rock-inhabiting, cosmopolitan, and species rich Teloschistaceae, with a diversity of growth habits ranging from crustose to fruticose. Our results confirm the use of a cumulative supermatrix approach as a viable method to generate comprehensive phylogenies summarizing relationships of taxa with multi-locus to single locus data. (C) 2012 Elsevier Inc. All rights reserved.

Se evaluaron seis regiones de ADN como posibles códigos de barras de ADN para Hongos, el segundo reino más grande de vida eucariota, por un consorcio multinacional y de laboratorios múltiples. La región de la mitocondria se utilizó la subunidad 1 de la citocromo c oxidasa como código de barras animal excluido como un marcador potencial, porque es difícil de amplificar en hongos, a menudo incluye intrones grandes y puede ser insuficientemente variable. Tres subunidades del cistrón de ARN ribosómico nuclear fueron en comparación con las regiones de tres genes de codificación proteica representativos (la subunidad más grande de la ARN polimerasa II, la segunda más grande subunidad de la ARN polimerasa II y mantenimiento de minicromosomas proteína). Aunque las regiones de genes que codifican proteínas a menudo tenían un porcentaje más alto de identificación correcta en comparación con ribosomal marcadores, baja amplificación por PCR y éxito de secuenciación eliminados ellos como candidatos para un código de barras universal para hongos. Entre la regiones del cistrón ribosómico, el espaciador transcrito interno (ITS) tiene la mayor probabilidad de identificación exitosa para la gama más amplia de hongos, con la brecha de código de barras más claramente definida entre la variación inter e intraespecífica. El nuclear subunidad ribosómica grande, un marcador filogenético popular en ciertos grupos, tuvieron una resolución de especies superior en algunos grupos taxonómicos, como los primeros linajes divergentes y las levaduras ascomicetas, pero por lo demás era ligeramente inferior al ITS. El ribosomal nuclear La subunidad pequeña tiene una resolución pobre a nivel de especie en los hongos. SU será propuesto formalmente para su adopción como el código de barras fúngico principal marcador al Consorcio para el Código de Barras de la Vida, con la posibilidad de que se desarrollen códigos de barras suplementarios para grupos taxonómicos estrechamente circunscritos., Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative proteincoding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

We validate two invalidly published species names, Ceriporia mpurii and C. pierii.

A short revision of the vagrant Aspicilia species of North America is presented based on morphological, molecular and ecological data. Vagrant Aspicilia are common lichens throughout the steppes of the western United States and in southwestern parts of Canada. Species delimitation of these lichens is difficult because of the paucity of morphological characters and large degree of variation. Inferences from nuITSrDNA sequences reveals that the North American specimens of A. fruticulosa are not most closely related to their Eurasian populations but instead share a unique ancestor with A. hispida. The specimens of A. fruticulosa from the New World are hereby recognized as a distinct species, A. rogeri. Its differentiation from the similar A. fruticulosa and A. hispida is discussed. The exclusion of A. fruticulosa from the N. American checklist is proposed temporarily.

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Department of Natural Sciences Gardner-Webb University Department of Biology Villanova University Potato Research Center Georgikon Faculty University of Pannonia Dipartimento di Biologia e Biotecnologia 'Charles Darwin' Sapienza Università di Roma Department of Earth and Planetary Sciences Johns Hopkins University Department of Environmental Science and Technology University of Maryland Department of Plant Medicine Chungbuk National University Hawai‘i Institute of Marine Biology University of Hawai‘i Institute of Marine Science University of Auckland Centre for Agricultural Research Hungarian Academy of Sciences Department of Zoology Eszterházy Károly University Herbarium School of Biological Sciences University of Reading Instituto de Ciencias Ambientales y Evolutivas Facultad de Ciencias Universidad Austral de Chile Department of Biosciences University of Helsinki Ornithological Nomenclature Expert Green Plant Herbarium Department of Natural History Royal Ontario Museum Nomenclature Specialist CITES Animals Committee; Turtle Conservancy Global Wildlife Conservation Department of Plant Anatomy Institute of Biology Eötvös Loránd University Department of Biosciences (Plant Biology) Viikki Plant Science Centre Illinois Natural History Survey Institute of Biodiversity Science and Sustainability California Academy of Sciences Royal Botanic Gardens Kew NTNU University Museum Norwegian University of Science and Technology Institut de Biologia Evolutiva Universitat Pompeu Fabra Bioveyda Biodiversity Inventories and Research Department of Plant Biology Ecology & Evolution and Herbarium Oklahoma State University Research School of Earth Sciencesn National Universityn Capital Territory Departamento de Biologia Animal Instituto de Biologia Universidade Estadual de Campinas Senckenberg Naturhistorische Sammlungen Department of Biology University of Copenhagen Department of Botany Smithsonian Institution National Museum of Natural History Plant Pest Diagnostics Branch California Department of Food and Agriculture PPG Zoologia Departamento de Zoologia Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Macleay Museum University of Sydney Centre for Ecology and Hydrology Edinburgh Research Station Laboratório de Coleções Zoológicas Instituto Butantan Environmental Management School of Applied and Biomedical Science Federation University PPG Biodiversidade Animal Universidade Federal de Santa Maria National Museum of Natural History Smithsonian Institution Department of Terrestrial Zoology Western Australian Museum Museu Nacional da História Natural e da Ciência Universidade de Lisboa The Kyoto University Museum Kyoto University Finnish Museum of Natural History (Botany) University of Helsinki Royal Botanic Garden Edinburgh School of Biological Sciences and Environment Institute University of Adelaide Nees Institut für Biodiversität der Pflanzen Universität Bonn Department of Plant Science and Biotechnology University of Pannonia Lee Kong Chian Natural History Museum National University of Singapore Denver Botanic Gardens Department of Biology Earlham College Montana Entomology Collection Montana State University School of Environmental Sciences University of Guelph Instituto de Ambiente de Montaña y Regiones Áridas Universidad Nacional de Chilecito Martha N. and John C. Moser Chair in Arthropod Systematics and Biological Diversity The Ohio State University Department of Biology Victor Valley College Identification and Naming Department Royal Botanic Gardens Kew Natural History Laboratory Faculty of Science Ibaraki University Natural History Museum and Botanical Garden University of Tartu Plant Protection Institute Centre for Agricultural Research Hungarian Academy of Sciences Department of Zoology Denver Museum of Nature & Science Department of Systematic and Evolutionary Botany Universität Wien FishBase Department of Zoology Swedish Museum of Natural History Department of Zoology Museo Civico di Storia Naturale of Verona Departamento de Zoologia Universidade Federal do Paraná Sezione di Zoologia degli Invertebrati e Idrobiologia MUSE-Museo delle Scienze di Trento Centro de Ciências Agrárias Ambientais e Biológicas Universidade Federal do Recôncavo da Bahia Department of Biological Sciences University of Toronto Department of Environmental Science and Policy George Mason University Natural History Museum of Geneva Department of Genetics and Evolution University of Geneva Departamento de Zoologia Universidade de Brasília Department of Integrative Biology Oregon State Arthropod Collection Oregon State University Henares 16 Velilla de San Antonio Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution International Committee on Bionomenclature Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias Jaboticabal Departamento de Biologia Aplicada à Agropecuária Faculty of Biology Alexandru Ioan Cuza University of Iași Departamento de Biología Universidad de Los Andes Laboratorio de Morfología Animal Universidad Autónoma del Estado de Hidalgo H.W. Manter Laboratory of Parasitology University of Nebraska-Lincoln Robert Bebb Herbarium (OKL) University of Oklahoma Oklahoma Biological Survey Department of Microbiology and Plant Biology Fiocruz Mata Atlântica Fundação Oswaldo Cruz Department of Civil and Environmental Engineering Ehime University Department of Zoology Hungarian Natural History Museum Department of Science Education Hiroshima University Department of Earth Sciences Natural History Museum Kazan Federal University Museum für Naturkunde Leibniz-Institut für Evolutions-und Biodiversitätsforschung Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos Universidad Tecnológica Indoamérica Integrated Taxonomic Information System National Museum of Natural History Smithsonian Institution Natural History Museum of Denmark Department of Botany Szent István University University of Sydney Zoological Museum of Lomonosov Moscow State University Biodiversity Institute University of Kansas CITES Scientific Authority Finnish Museum of Natural History (Botany) University of Helsinki Instituto de Botânica Department of Entomology Kerala Agricultural University University of Michigan Herbarium EEB Chelonian Research Foundation Turtle Conservancy Instituto de Ciencias Marinas y Limnológicas Facultad de Ciencias Universidad Austral de Chile Kansas Biological Survey and the Biodiversity Institute University of Kansas Laboratório de Ecologia e Conservação Universidade Federal do Mato Grosso do Sul Sciences Department Museums Victoria Department of Biology and Museum of Vertebrate Biology Portland State University Department of Biological Sciences Texas Tech University Staatliches Museum für Naturkunde Stuttgart Department of Bioinformatics and Genetics Swedish Museum of Natural History Laboratorio de Sistemática y Biología Comparada de Insectos Instituto de Ciencias Naturales Universidad Nacional de Colombia Global Biodiversity Information Facility Fragile Inheritance Natural History National Focal Point to the Convention on Biological Diversity Royal Belgian Institute of Natural Sciences Department of Biology Pittsburg State University Departamento de Zoologia Instituto de Biociências Universidade de São Paulo Agricultural Research Council Plant Protection Research Instituten National Collection of Insects Section of Mollusks Carnegie Museum of Natural History Department of Zoology Faculty of Science Charles University Museo Argentino de Ciencias Naturales Bernardino Rivadavia National Parks Board Botanic Gardens Department of Ecology and Evolutionary Biology University of Kansas Judicial Commission on Prokaryote Nomenclature Botanische Staatssammlung München and SNSB IT Center Staatliche Naturwissenschaftliche Sammlungen Bayerns Permanent ICN Nomenclature Committee for Fungi International Mycological Association Museo Nacional de Ciencias Naturales (CSIC) Dipartimento di Scienze della Vita e Biologia dei Sistemi Università di Torino Istituto per la Protezione Sostenibile delle Piante sez. di Torino CNR Department of Environmental Sciences University of Basel Allwetterzoo Münster Department of Biology University of Hawai'i at Manoa UNC Herbarium (NCU) North Carolina Botanical Garden University of North Carolina at Chapel Hill Abteilung Morphologie und Systematik der Tiere und Zoologisches Museum Universität Göttingen Unité Mixte de Recherche Peuplements Végétaux et Bioaggresseurs en Milieu Tropical Université de La Réunion Essig Museum of Entomology University of California Berkeley General Committee for Nomenclature [for algae fungi and plants] Royal Botanic Gardens and Domain Trust Smithsonian Marine Station Molecular Ecology and Fisheries Genetics Lab School of Biological Sciences Bangor University Department of Entomology Entomology Research Museum University of California Australian National Insect Collection CSIRO National Research Collections Australian Capital Territory School of Life Sciences Biodiversity Knowledge Integration Center Hasbrouck Insect Collection Arizona State University Landcare Research School of Biological Sciences University of Auckland Institute of Zoology Chinese Academy of Sciences, Chaoyang District Laboratório de Ictiologia Departamento de Zoologia IBB-UNESP Campus de Botucatu Universidade Estadual Paulista (Unesp) Faculdade de Ciências Agrárias e Veterinárias Jaboticabal Departamento de Biologia Aplicada à Agropecuária

We provide a phylogenetic revision of the Pseudocyphellaria crocata complex in the Americas. Specimens traditionally identified as P. crocata, based on their cyanobacterial photobiont, yellow pseudocyphellae, at least partially white medulla, and yellow soralia or soralia-like structures, are shown to represent 13 distinct species, forming a monophyletic group divided into four large clades, three comprising one species each and one containing eight species, plus two taxa for which no molecular data are available. Seven species correspond to what was previously recognized as P. crocata and one to P. dozyana, whereas a further one is identified as the sorediate counterpart of the usually apotheciate taxon P. lechleri and another as a pseudosorediate morph of the usually phyllidiate species P. neglecta. Surprisingly, none of the species represents P. crocata s.str., which must therefore be excluded from the American lichen biota. The 13 recognized species include three species new to science and th...

A new genus Puttea S. Stenroos & Huhtinen is described for the lichen species formerly known as Fellhanera margaritella (Hulting) Hafellner. The study was based on phylogenetic analyses of the mtSSU as well as on anatomical and ecological investigations. Puttea is characterized by its inconspicuous thallus, gelatinized exipulum of radiating hyphae, hemiamyloid asci of the Psora-type arising from croziers, non-septate spores and a crystalline layer covering the hymenium and excipulum. The currently monospecific genus grows almost exclusively on the liverwort Ptilidium pulcherrimum and has so far been reported from Austria, the Czech Republic, Finland, Norway, Russia, Slovakia, Sweden and Switzerland. The taxonomic position of Puttea could not be reliably assessed but in the present analyses it appears, together with Lecidea hypopta, in a clade comprising the Sphaerophoraceae, Psoraceae, Ramalinaceae and Pilocarpaceae.

Fourteen genera belong to a monophyletic core of cetrarioid lichens,Ahtiana, Allocetraria, Arctocetraria, Cetraria, Cetrariella, Cetreliopsis, Flavocetraria, Kaernefeltia, Masonhalea, Nephromopsis, Tuckermanella, Tuckermannopsis, UsnocetrariaandVulpicida. A total of 71 samples representing 65 species (of 90 worldwide) and all type species of the genera are included in phylogentic analyses based on a complete ITS matrix and incomplete sets of group I intron, β-tubulin, GAPDH and mtSSU sequences. Eleven of the species included in the study are analysed phylogenetically for the first time, and of the 178 sequences, 67 are newly constructed. Two phylogenetic trees, one based solely on the complete ITS-matrix and a second based on total information, are similar, but not entirely identical. About half of the species are gathered in a strongly supported clade composed of the generaAllocetraria, Cetrarias. str.,CetrariellaandVulpicida.Arctocetraria,Cetreliopsis,KaernefeltiaandTuckermanellaare monophyletic genera, whereasCetraria, FlavocetrariaandTuckermannopsisare polyphyletic. The taxonomy in current use is compared with the phylogenetic results, and future, probable or potential adjustments to the phylogeny are discussed. The single non-DNA character with a strong correlation to phylogeny based on DNA-sequences is conidial shape. The secondary chemistry of the poorly known speciesCetraria annaeis analyzed for the first time; the cortex contains usnic acid and atranorin, whereas isonephrosterinic, nephrosterinic, lichesterinic, protolichesterinic and squamatic acids occur in the medulla. Notes on the anatomy ofCetraria annaeandFlavocetraria minusculaare also provided.

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

We have revisited the phylogenetic evaluation of the Physcia aipolia—P. caesia lichen group (sect. Caesiae; Physciaceae, Lecanorales) in order to investigate whether new sequence data and extensive sampling can help us to understand the phylogenetic relationships in that group. We combined partial mtSSU DNA data with two previously used nuclear gene regions (betatubulin, ITS) and a group I intron. We also compared the resulting phylogenies with chemical and morphological characters. Altogether 52 specimens of the P. aipolia—P. caesia group were analysed. Direct optimization of the molecular data revealed several well-supported groups. Our results essentially agreed with those of the earlier studies, and we were able to confirm the independent taxonomic status of some controversial morphotaxa. We also discovered at least two distinct clades that potentially represent species new to science. A new nomenclatural combination, Physcia alnophila (Vain.) Loht., Moberg, Myllys & Tehler, is proposed.

The monotypic genus Fuscoscypha possesses hairs similar as in the genus Hyaloscypha but differs by grey-olivaceous-brown apothecia with short dark stipes. Molecular data proves that the pigmentation does not permit delimitation of a separate genus, as white and brown taxa do not form separate clades. Followingly, Fuscoscypha is here considered to be a synonym of Hyaloscypha. Three of the here treated four species have an olivaceous-brown excipulum. Two are saprophytes on decaying leaves and fruits of angiosperms: F. acicularum, the type species of Fuscoscypha, and Hyaloscypha fuscostipitata comb. nov. (formerly placed in Betulina). Two are biotrophic parasites on Bryophyta: Hyaloscypha hepaticola comb. nov. (formerly placed in Trichopeziza) and the hyaline-excipled Hyaloscypha albocarpa spec. nov. which is otherwise very similar to H. hepaticola. The type species of the genus Betulina, B. hirta, is found to be an earlier synonym of Urceolella salicicola (= U. graddonii). The new combination Urceolella hirta is therefore proposed, hence Betulina is considered a synonym of Urceolella.

The phylogeny of the lichen genera Anaptychia (Physciaceae, Euascomycetes) and Physconia was studied using nucleotide sequences of the mitochondrial ribosomal small subunit (mtSSU rDNA) and the internal transcribed spacers of the nuclear ribosomal repeat (ITS). Phylogenetic analyses of the combined data set demonstrated that all included eight Anaptychia species formed a monophyletic group, as did the species of Physconia. The two gene regions revealed qualitatively similar relationships within the genus.

The selectivity of mycobionts and cyanobionts in lichen symbioses were examined. We analyzed symbiotic cyanobionts, collected from different sample sites, and compared them to free-living cyanobacteria Nostoc. Cyanobionts were obtained from lichens assigned to the genera Pseudocyphellaria and Sticta, in particular. Multiple gene loci were screened and direct optimization was used in the phylogenetic analyses. We show that many lichen fungi are strongly selective towards their cyanobionts. Lichenized ascomycetes seem to be able to identify and choose a specific strain, species or a species group of Nostoc with which to associate. The present analyses also suggest that some of the Nostoc taxa may be specialized in symbiotic life with only lichenized ascomycetes. Despite the selectivity observed in fungi, there appears to be no coevolution between the partners. We have also discussed the problems of using the tRNA(Leu) intron as a marker in phylogenetic analyses. (Less)

The phylogenetic relationships of the lichenised ascomycete family Stereocaulaceae were investigated with partial beta-tubulin, partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and SSU rDNA sequence data. Due to the marked length variation in the SSU rDNA sequences, the analyses were performed with direct optimization. The combined analysis of the beta-tubulin, GAPDH and SSU rDNA sequences as well as the separate analyses of beta-tubulin and GAPDH data recognized the monophyletic group comprising Lepraria, Muhria and Stereocaulon. In the combined analysis Stereocaulon tornense appears as a basal taxon in the Stereocaulon clade, suggesting that the crustose growth form and the absence of cephalodia are primitive features within the genus. Muhria is nested in Stereocaulon and groups with the crustose S. cumulatum and S. leucophaeopsis. The genus Lepraria is monophyletic if Leproloma is included, but species that were represented by several specimens in our study, i.e., Lepraria jackii and Leproloma membranaceun, do not appear as monophyletic entities. The genus Pilophorus is included in Cladoniaceae. Combined analysis of the three data-sets clearly led to an increase in support values compared to the separate analyses, showing high support for the monophyly of families Cladoniaceae and Stereocaulaceae and for the sistergroup relation for the two families. The relationships between higher groupings did not reach high support values probably due to the incongruencies among the three datasets. (Less)

Phylogenetic relationships within the Parmeliaceae are analysed cladistically on the basis of DNA characters from partial β-tubulin, partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and ITS sequences. 100 taxa representing 73 of the 88 genera currently recognised are included in the analyses. Eight monophyletic groups including two or more genera were identified in the tree calculated from the combined data matrix. Three of the groups cover almost half of the species of the family. The largest and strongest supported group includes seven genera with their distribution centres in the Southern Hemisphere: Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Xanthomaculina and Xanthoparmelia. The second group is a clade of four essentially tropical genera: Concamerella, Flavoparmelia, Parmotrema and Rimelia. The third large group with strong support is the core of cetrarioid lichens, distributed primarily in cold areas of the Northern Hemisphere. The genus Parmelia sensu Hale is not closely related with most of its segregates. One new combination, Cetrariella commixta, is proposed. Coelopogon abraxas is reported from South America for the first time.

Lichens consist of a fungal component that associates with either a green alga or cynobacterium, resulting in diverse morphologies. Resynthesis experiments of isolated myco- and photobionts, as well as internal transcribed spacer (ITS) rDNA phylogenies, suggest that the notoriously dissimilar photomorphs of Lobaria fendleri (Tuck. ex Mont.) Lindau and Lobaria amplissima (Scop.) Forss. both have a single mycobiont, which can simultaneously lichenize two unrelated photobionts, a eukaryote and a prokaryote. In the phylogenetic analyses, the genera Sticta and Durietzia appear monophyletic; whereas Lobaria and Pseudocyphellaria are both nonmonophyletic. Furthermore, the phylogenetic relationships of Durietzia, Lobarina, and Sticta relative to Lobaria and Pseudocyphellaria are in need of re-evaluation.Key words: internal transcribed spacer (ITS), photosymbiodeme, phylogeny, lichen-forming fungi, Lobaria amplissima, Lobaria fendleri, Pseudocyphellaria, Sticta.

Phylogenetic relationships within the family Parmeliaceae (lichenized ascomycetes) with emphasis on the heterogeneous group of cetrarioid lichens are reconstructed. The results are based on cladistic analyses of DNA-sequences, morphological and chemical data. Almost all currently recognized cetrarioid genera were included in the analyses together with parmelioid and alectorioid members of the presumably monophyletic family Parmeliaceae. We tried to sample taxonomic diversity of the family as widely as possible. The ITS1-5.8S-ITS2 region of the rDNA and a partial beta-tubulin gene from 126 samples representing 82 species were analysed. Cetrarioid lichens were identified as a monophyletic group, supported by both ITS and beta-tubulin characters. This group was reanalysed using 47 morphological, anatomical and secondary chemistry characters combined with the DNA data matrix. ITS and beta-tubulin sequences provide congruent information, and a clear correlation between DNA-data and conidial shape is observed. The current taxonomy of the cetrarioid lichens is discussed and compared with the phylogenetic trees obtained here. A comprehensive study of the phylogeography of some bipolar or subcosmopolitic species with representatives from both hemispheres was performed. Cetraria aculeata is the only taxon where correlation between DNA-data and geographic origin is observed.

Parsimony analyses of SSU rDNA sequences were conducted to examine phylogenetic relationships of selected genera within the families Cladoniaceae, Stereocaulaceae, Icmadophilaceae and Baeomycetaceae (lichen-forming ascomycetes). The analyses included 93 taxa (84 species) representing various groups of ascomycetous fungi. Analyses of the matrix with pre-aligned sequences were performed using heuristic and parsimony ratchet searches, and support values for the same matrix were calculated using parsimony jackknifing. The results support the recognition of the four families. Cladoniaceae are recircumscribed to accommodate Cladia, Cladonia, Heterodea, Metus, Pilophorus, Pycnothelia, Ramalea, Thysanothecium and the newly erected genus Carassea. Myelorrhiza is excluded from the family, while the status of other potential members, Calathaspis, Gymnoderma s.str. and Squamella, remains unresolved. Baeomycetaceae include Baeomyces and Phyllobaeis. Stereocaulaceae include Stereocaulon only, although the status of Muhria is still unclear. Finally, Icmadophilaceae include Dibaeis, Endocena, Knightiella, Icmadophila, Siphula and Thamnolia, while the status of Pseudobaeomyces and Siphulella requires further elucidation. The genus Cladonia appeared to be a polyphyletic assemblage, and accordingly, a new genus Carassea S. Stenroos, gen. nov., represented by C. connexa (Vain.) S. Stenroos, comb. nov., is described. Carassea is most closely related to Pycnothelia and Metus in the Cladoniaceae. Siphula, represented in the present analysis by six species, is not monophyletic, and is in need of reclassification.

Primers for amplification and sequencing of partial glyceraldehyde-3-phosphate dehydrogenase (gpd) gene were designed for lichenized fungi. The 5’ gpd primer is most probably fungal specific, since a BLAST search in GenBank found identical sequences only from ascomycetous taxa, whereas the 3’ gpd primer was more universal. Utility of the gpd primers and previously designed beta-tubulin primers was tested in nine lichen taxa. Both the gpd and beta-tubulin primer pairs amplified in most of the taxa examined: the gpd primers generated a c. 1100 nucleotide fragment, whereas the PCR product obtained from the beta-tubulin primers was c. 900 nucleotides long. The gpd amplification products of Cladonia arbuscula and C. rangiferina were sequenced and both were found to contain three introns, the length of which varied between 49 to 83 nucleotides. To examine the applicability of gpd sequences in resolving relationships within Ascomycota, trees were calculated from 22 fungal gpd sequences obtained from GenBank together with the two Cladonia sequences using parsimony jackknifing. The gpd tree was compared with the SSU rDNA tree of the respective species (or genera). A similar analysis of the beta-tubulin gene was not performed, because only a few beta-tublin sequences from the same taxa were available in GenBank. The gpd tree was well resolved but in conflict with the SSU rDNA tree. In contrast to the SSU rDNA tree, the gpd tree did not support the monophyly of the Ascomycota. Analysis of the combined data set produced a tree very similar to that of the SSU rDNA data. However, the relationship of Lecanorales to the other orders remained unresolved. Even though gpd and beta-tubulin are highly conserved proteins, the third codon positions and introns are variable and both genes have the potential for inferring phylogenetic relationships at the lower taxonomic levels in the lichenized fungi. The two genes may be useful even below species level, depending on the species investigated.

The subclass Chaetothyriomycetidae (Eurotiomycetes, Ascomycota) is an assemblage of ecologically diverse species, ranging from mutualistic lichenised fungi to human opportunistic pathogens. Recent contributions from molecular studies have changed our understanding of the composition of this subclass. Among others, ant-associated fungi, deep-sea fungi and bryophilous fungi were also shown to belong to this group of ascomycetes. The delimitation of orders and families within this subclass has not previously been re-assessed using a broad phylogenetic study and the phylogenetic position of some taxa such as the lichenised family Celotheliaceae or the Chaetothyrialean bryophilous fungi is still unclear. In our study, we assemble new and published sequences from 132 taxa and reconstruct phylogenetic relationships using four markers (nuLSU, nuSSU, mtSSU and RPB1). Results highlight several shortfalls in the current classification of this subclass, mainly due to un-assigned paraphyletic taxa. The family Epibryaceae is therefore described to circumscribe a previously un-assigned lineage. Celotheliales ad int. is suggested for the lineage including the lichen genus Celothelium and various plant pathogens. The delimitation of the family Trichomeriaceae is also broadened to include the genus Knufia and some anamorphic taxa. As defined here, Chaetothyriomycetidae includes four orders (Celotheliales ad int., Chaetothyriales, Pyrenulales, and Verrucariales) and ten families (Adelococcaceae, Celotheliaceae, Chaetothyriaceae, Cyphellophoraceae, Epibryaceae fam. nov., Herpotrichiellaceae, Pyrenulaceae, Requienellaceae, Trichomeriaceae, and Verrucariaceae).

Bryophilous ascomycetes are an overlooked and poorly known fungal group. In this study, the extreme and small-sized niche of Polytrichum piliferum hyaline leaf tips was screened for the presence of these fungi in Finland. Three closely related species were found. Bryochiton perpusillus and Bryochiton monascus were identified from several samples, and DNA isolations revealed a third closely related species, Bryochiton sp. In addition, melanised hyphae, typical to the Bryochiton species, were present in all the samples. According to phylogenetic analyses consisting of combined small subunit (SSU), large subunit (LSU), and 5.8S rDNA sequences, and internal transcribed spacer (ITS) rDNA sequences, the species showed affinity with Teratosphaeriaceae within Capnodiales, and especially with black, meristematic species often inhabiting rock substrate in extreme environments. The connection was supported by meristematic growth of the Bryochiton species in culture. Bryochiton is the second sexual genus associated within the family Teratosphaeriaceae, and B. perpusillus, and B. monascus constitute examples of teleomorphs within a group of meristematic anamorphs. These findings emphasize the multiform diversity underlying poorly researched fungal groups, such as the bryophilous fungi.

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi., B.R. and C.L.S. acknowledge support from the Intramural Research Program of the National Institutes of Health, National Library of Medicine

To examine phylogenetic relationships among the "cladoniiform" lichenized fungi, i.e., the families Cladoniaceae, Baeomycetaceae, Icmadophilaceae, Stereocaulaceae, and Siphulaceae, and to provide evidence for the anticipated independent origins of podetia and pseudopodetia, we conducted phylogenetic analyses of SSU (small subunit) rDNA sequences from 39 lichen-forming fungi. These fungi represent all of the major growth forms of lichen associations, fruticose (including "cladoniiform"), foliose, and crustose. Our analysis suggests that lichen-forming fungi with a "cladoniiform" morphology arose multiple times within the ascomycetes. Additionally, each of the other thallus growth forms, crustose, foliose, and fruticose, have originated multiple times. It also seems to be clear that neither all podetiate nor all pseudopodetiate taxa form a monophyletic group. Therefore the term "podetium" should be restricted to homologous structures that are most probably limited to the genera Cladonia, Cladina, Pycnothelia, and allies. The "pseudopodetia" of Stereocaulon (Stereocaulaceae) and Cladia (Cladiaceae) may represent different states of the same homologous character. Our phylogenetic hypothesis supports the monophyletic origin of the order Lecanorales sensu stricto, including representatives of five suborders Cladoniineae, Lecanorineae, Teloschistineae, Agyriineae and Peltigerineae, but excluding representatives of the suborders Acarosporineae (Acarospora schleicheri and Megaspora verrucosa), Pertusariineae (Pertusaria trachythallina), and Umbilicarineae. The suborder Cladoniineae and the family Cladoniaceae both appear to be polyphyletic assemblages.